It's up to you. The final MKV is at least a week away, because the rendering will take days. The AVCHD will probably follow about a week later.
Also, yes, in order to use MKV in TS Muxer, you need to demux the separate video and audio streams from it. MKVExtract (part of the MKVToolnix) is a good tool. Or as CatBus said, Yamb would probably also do the trick, although it's a little slow.
As to the chapters, I suppose I'll add the chapter files someone sent me (sorry don't remember who) to all the releases.